1 And This is How it Ends
by SheWhoWaits
Summary: Set just before and after TATM. Amy confesses her deepest secret accidentally and then has to make a choice. Neither option is one she wants to make. She will break his heart and she'll break it again and again and that break will be a fixed point in time forever. Won't it? Alternate Endings, OCC-ness does occur a little. Amy/Eleven 3 for sure :) Enjoy :)
1. Undone

_A/N:_

_This part of the story is set BEFORE The Angels Take Manhattan, River is not mentioned much in this Fic and she is also not married to the Doctor._  
_This fic may not run allong the same time lines or story plot as the Show and so may be AU in some places however dispite that eveything happened as it did._

_Sorry in advance for any gaps in the story where it doesnt fit the real Who Universe but enjoy :P_

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**Undone**

The TARDIS was quiet, just the gentle hum of the engines and the usual vworping sound as she drifted through the vortex. The control room was dark, empty, just illuminated dimly by the console, a gentle gold glow mixing with the faint blue light from under the glass floor. A much different look to that of the TARDIS in the day (not that it had days or nights but everyone has to sleep sometime), busy, madding in the best of ways, full of energy and life. But now it was quiet and the only thing that disturbed the peace was a gentle but saddened voice.

"Oh Rory, my sweet, loving, roman Rory…I am so sorry…Its always been him…always…I'm sorry…" her voice, Amy Ponds voice trailed down into a small sigh as she felt the tears run hot down her face burning into her skin the way her heart burned for so many reasons. She could feel her mascara reduced to a watery line down her face running from her like she had run from so much. There she was, sat down on the floor, curled up with her head in her hands. Amy Pond alone and completely undone.

After the tears had dried and she'd wiped the mascara from her cheeks she looked up for the first time to see him in the shadows. She didn't know how long he had been there, standing just behind the console, the dim lighting illuminating the anger on his face.

"Its always been _him_." His calm voice whispered, questioning the statement with his tone. Amy choked on newly formed tears a lump rising in her throat. He'd heard her deepest secret, she didn't want him to know, he was happier not knowing.

"Always HIM?"

"I'm sorry…" Amy choked again "I never meant for you to… for you to hear that… please…" He walked around the console coming into the light, staring down at her.

"Mr. I-waited-two-thousand-years-for-you and all you can say is that it was _ALWAYS_ HIM?!" He shouted at her, the sound of his voice scared her he wasn't like this, not to her. The sound echoed around the empty room, ringing out for what seemed hours to Amy. Once it stopped and the quiet had returned his voice softened back to its usual tone.

"Question is…What are we going to do about it Pond?"

**XXXX**

Amy was standing up against the safety rail in the control room as the Doctor and Rory laughed and joked. Their voices filling the air as usual, bring the room back to life. The doctor was explaining something to do with a contraption on the console with his usual "imagine a…. actually don't because its nothing like that" while Rory laughed along at the ridiculous explanation.

Amy wasn't even paying attention, she was staring at the floor, so hard she was staring through it to the floor beneath the glass one, more detached from the room than the TARDIS was to linear timelines. Then a voice cut through and she jumped to life.

"Amy? What's up? You seem quiet…" Rory asked walking over putting his hands on her arms and looking deeply into her eyes, face screwed up with concern. Amy must have taken a second too long to answer because the Doctors voice came ringing out and her gaze locked onto him over Rory's shoulder.

"I'm sure she's fine Rory, just had a late night… didn't we Amelia?" The usual tone light, playful but she couldn't help but hear the seriousness in his voice that lightly threatening tone that she only could recognize. He had called her Amelia, he only did that when he was worried or serious. She watched as his playful smile turned to his serious face. She could have sworn she saw a look in his eye, one she hadn't seen before and before she could work out what it was, it was gone. Just like that and his face had returned to its ever happy state, that of a child in a sweet shop.

She realized she had been silently staring for too long because Rory had begun to look between the two of them. He never could get on that level with them, Amy and the Doctor communicating with just a look. And he hated it but before Rory could ask the Doctor began throwing the TARDIS into full flight, shouting about new worlds, asking question after question about who and what and why and pulling timey wimey things and wibbly leavers and Rory forgot to ask what ever it was he was going to ask.

**XXXX**

"Amy what did he mean by we?" Rory asked Amy when they were alone in the TARDIS after a day lost in the Ziron galaxy floating around from planet to planet trying to satisfy the Doctors need to see something 'Tastefully amazing but not too showy off' and Amy's need for non alien food.

"Really Rory, you want to do this now? I'm tired from today please can we leave the conversations about you questioning the Doctor until I haven't just been nearly poisoned by an alien pizza?" she said in a half joking half serious voice. She moved her hair out of her face and stared at Rory blank faced.

"Em yes I do, what did he mean by we? Did you go somewhere? Without me?"

"No stupid face, how could you even think that. He was using it to talk about me, the way he always does when he calls me Amelia."

"Sorry."

"Yeah well you should be. When will you realize that I want _you_?" she said walking off, holding back the tears. She felt so angry with herself, with Rory, with the Doctor. But most of all she felt disgust. Amelia Pond was disgusted with herself for what had happened.


	2. Amys Final Farewell

**_This chapter is set at the end of The Angels Take Manhattan. Its an Alternate Ending which is pretty sad really. Enjoy. PLEASE Review :)_**

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"Then say it… SAY IT! Say it and I'll stay!" He looked at her, lips quivering so scared, she'd never seen him scared like this. Her eyes begged him to say it, so she could stay because she wanted to stay.

"Amelia Pond… MY Amelia Pond… I…I…" he stuttered and stammered, the sentence echoed in his memory it reminded him slightly of a moment so similar but from so long ago. He was so torn between loving her and knowing how much pain he'd end up causing or letting her go where she could at least grow old with someone who could give her so much more than the stars. The look of defeat showed on his face, he looked like everything that made him her raggedy man had faded, gone out like a sun burning out. Like someone had just turned out a light. She sighed, one of relief or one of sorrow she didn't know.

"Im sorry Doctor… My Doctor I love you… but this is goodbye." She kissed him on the lips, the most sweet and painful kiss telling him everything he needed to know. Telling him goodbye, that she loved him, that she'll miss him. He kissed her back with everything he had, telling her what he couldn't say, what was too dangerous to say. He just hoped she could understand.

As they pulled away he looked at her with a smile.

"Its time to stop waiting….Amy Williams." He gave her the biggest false smile he could, something so she could go without feeling too guilty, to sad. She nodded back, tears streaming down her face. That beautiful face that he'd never ever get to see again. As she stepped back he grabbed her back again. Pressing something into the palm of her hand. It was cold, metal and had a sharpish edge. "Never let it go." He whispered and then she was gone. She was gone and he didn't even say goodbye, not properly. The Doctor walked back into the TARDIS so angry with himself… three words that's all he had to say and she would have been here, with him off to some new world, some amazing planet. But he couldn't because that wasn't fair. And here he was again…

Alone.

XXXXX

In his hand he held the last hope of his love, the last chance to listen to Amelia Pond, the girl who waited, waited her whole life for him.

_Hello Old Friend._

_I'm sorry, so sorry I never stayed. I promised forever and I broke that. If you knew how much I regret not staying Doctor… But thank you for the Key, my little bit of you and that life that I can keep forever. Thank you. _

_I have Rory but he knows, he knows he's not enough. He knows I want you. I want my raggedy man to turn up and take me in my nightie to see the stars. But he pretends just like I do that he's happy. _

_Raggedy man please come, please turn up in my garden, on my street. Please. _

_I know you told me to stop waiting, I nodded and agreed but the truth is, I'm Amelia Pond – The girl who waited. The girl who's waiting. For you. _

_I know you'll never come and that's not your fault, never your fault. I made my choice and now ill live with it. So carry on Doctor, my Doctor travel and see the stars and find someone to show it all too. Make them see everything I've seen and more. Because by the time you read this, my story will be over, I wont be remembering anymore so make someone else have something to remember._

_One last thing. Somewhere there's a little girl waiting for you in her garden. Find her, tell her everything, give her hope that she's waiting for something that will happen. Tell her "this is the story of Amelia Pond… and this is how it ends."_

_Goodbye Doctor because __**this**__ is how it ends. _

"Not if I can help it."

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_**So as you can **_**_probably tell the ending means... a SEQUEL!  
And for those of you wondering about what happened in between these two chapters between the Doctor and Amy the night she confessed then just keep watching... there will be a one shot up about that too! :D gotta leave you guessing some how!_**

**_Please Review and Comment, Let me know what you think!  
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